The structure of a polygamous repressor reveals how phage-inducible chromosomal islands spread in nature

Abstract

Stl is a master repressor encoded by Staphylococcus aureus pathogenicity islands (SaPIs) that maintains integration of these elements in the bacterial chromosome. After infection or induction of a resident helper phage, SaPIs are de-repressed by specific interactions of phage proteins with Stl. SaPIs have evolved a fascinating mechanism to ensure their promiscuous transfer by targeting structurally unrelated proteins performing identically conserved functions for the phage. Here we decipher the molecular mechanism of this elegant strategy by determining the structure of SaPIbov1 Stl alone and in complex with two structurally unrelated dUTPases from different S. aureus phages. Remarkably, SaPIbov1 Stl has evolved different domains implicated in DNA and partner recognition specificity. This work presents the solved structure of a SaPI repressor protein and the discovery of a modular repressor that acquires multispecificity through domain recruiting. Our results establish the mechanism that allows widespread dissemination of SaPIs in nature.

Non-canonical Staphylococcus aureus pathogenicity island repression

“…4A). We used this region because in all characterised SaPIs the Stl proteins bind to the region that lies between stl and str(5) (9) and our reporter assays showed as regulated by Stl. The detailed analysis of the protected regions identified 8 putative Stl binding sites, organised as 4 different putative operators (1-4) (Fig.…”

“…Thus, the inducers for SaPIbov1, SaPI1 or SaPI2 are the phage-encoded dUTPases, Sri or recombinase proteins, respectively (4)(5)(6). Because of the singularity of the induction-repression mechanism present in the SaPIs, and to gain more insight into this interesting system, we recently solved the structure of the SaPIbov1 Stl (Stl SaPIbov1 ) repressor alone and in complex with two different inducing proteins, the dimeric and trimeric dUTPase proteins encoded by phages O11 and f11, respectively (9). Our studies revealed that Stl SaPIbov1 is a canonical dimer, with a modular structural organisation reminiscent of that previously reported for many phage-and other MGE-encoded repressors, including the CI repressor from the archetypical phage l (9, 10).…”

“…The copyright holder for this this version posted September 7, 2021. ; https://doi.org/10.1101/2021.09.07.459249 doi: bioRxiv preprint dimer, activating either the lytic cycle of the prophages or the transfer of the different MGEs (11,12). In the case of SaPIbov1, the only SaPI structurally characterised so far, the Stl SaPIbov1 dimer is also disrupted, a process that in this case occurs after the interaction of Stl SaPIbov1 with its cognate phage-encoded inducer proteins (9).…”

Non-canonical Staphylococcus aureus pathogenicity island repression

“…Thus, the inducers for SaPIbov1, SaPI1 or SaPI2 are the phage-encoded dUTPases, Sri or recombinase proteins, respectively ( 4–6 ). To gain more insight into this interesting and distinctive induction-repression mechanism of the SaPIs, we recently solved the structure of the SaPIbov1 Stl (Stl SaPIbov1 ) repressor alone and complexed with two different inducing proteins: the dimeric and trimeric dUTPase proteins of phages O11 and ϕ11, respectively ( 9 ). Our studies revealed that Stl SaPIbov1 is a canonical dimer, with a modular structural organization reminiscent of many well-studied phage and MGE repressors, including the CI repressor of archetypical phage λ ( 9 , 10 ).…”

“…To gain more insight into this interesting and distinctive induction-repression mechanism of the SaPIs, we recently solved the structure of the SaPIbov1 Stl (Stl SaPIbov1 ) repressor alone and complexed with two different inducing proteins: the dimeric and trimeric dUTPase proteins of phages O11 and ϕ11, respectively ( 9 ). Our studies revealed that Stl SaPIbov1 is a canonical dimer, with a modular structural organization reminiscent of many well-studied phage and MGE repressors, including the CI repressor of archetypical phage λ ( 9 , 10 ). These repressors have N-terminal domains that recognize and bind to their cognate DNA operator regions, and C-terminal domains that are involved in repressor dimerization and inducer recognition.…”